Analysis of the algorithm: From rankings to backup genes.

Ranking section

For each of the affected genes present in the list, a ranking with the score and percentile of every possible gene was obtained. Once this was done, the position for every known backup gene was obtained and the statistical descriptor of all the values calculated.

Table 1. Performance summary for every kernel and net before integration.

Net Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
biological_process ct 1 1 1 1 0.958333333333333
biological_process el 1 1 1 1 0.958333333333333
biological_process ka 1 1 1 1 0.958333333333333
biological_process node2vec 1 1 1 1 0.958333333333333
biological_process rf 1 1 1 1 0.958333333333333
disease ct 1 1 1 1 0.958333333333333
disease el 1 1 1 1 0.958333333333333
disease ka 1 1 1 1 0.958333333333333
disease node2vec 1 1 1 1 0.958333333333333
disease rf 1 1 1 1 0.958333333333333
genetic_interaction_weighted ct 1 1 1 1 0.96
genetic_interaction_weighted el 1 1 0.666666666666667 1 0.96
genetic_interaction_weighted ka 1 1 0.666666666666667 1 0.96
genetic_interaction_weighted node2vec 1 1 1 1 0.96
genetic_interaction_weighted rf 1 1 0.833333333333333 1 0.96
molecular_function ct 1 1 0 1 0.923076923076923
molecular_function el 1 1 0 1 0.923076923076923
molecular_function ka 1 1 0 1 0.923076923076923
molecular_function node2vec 1 1 0 1 0.923076923076923
molecular_function rf 1 1 0 1 0.923076923076923
pathway ct 0.551724137931034 1 0.333333333333333 1 0.918032786885246
pathway el 0.482758620689655 1 0.166666666666667 1 0.935483870967742
pathway ka 1 1 1 1 0.90625
pathway node2vec 1 1 0.5 1 0.90625
pathway rf 0.448275862068966 1 0.166666666666667 1 0.935483870967742
phenotype ct 1 1 0 1 0.956521739130435
phenotype el 1 1 0 1 0.956521739130435
phenotype ka 1 1 1 1 0.956521739130435
phenotype node2vec 1 1 1 1 0.956521739130435
phenotype rf 1 1 0 1 0.956521739130435
protein_interaction ct 0.902430555555556 1 0.166666666666667 1 0.972602739726027
protein_interaction el 0.861111111111111 1 0.166666666666667 1 0.972602739726027
protein_interaction ka 1 1 0.833333333333333 1 0.96
protein_interaction rf 0.902777777777778 1 0.166666666666667 1 0.972602739726027

Table 2. Performance summary for every kernel after integration

Integration Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
integration_mean_by_presence ct 1 1 0.666666666666667 1 0.96
integration_mean_by_presence el 1 1 0.333333333333333 1 0.96
integration_mean_by_presence ka 1 1 0.5 1 0.96
integration_mean_by_presence node2vec 1 1 1 1 0.96
integration_mean_by_presence rf 0.625 1 0.5 1 0.966442953020134
mean ct 1 1 0.666666666666667 1 0.96
mean el 1 1 1 1 0.96
mean ka 0.736111111111111 1 0.333333333333333 1 0.965986394557823
mean node2vec 1 1 1 1 0.96
mean rf 1 1 1 1 0.96

Backup Pairs Coverage By Layer

Backup Pairs Coverage By Layer

Backup Pairs Coverage By Layer

Backup Pairs Coverage By Layer

Backup Pairs Coverage By Layer

CDF plots of non integrated kernels

ROC plots of integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels